Abstract: 【Objective】This paper explored the impact of deep tillage cultivation on the yield and production value of flue-cured tobacco, as well as the characteristics of rhizosphere soil and the micro-ecosystem. The aim was to provide scientific evidence for the construction of a reasonable cultivation layer and the establishment of a high-quality and efficient cultivation system for flue-cured tobacco in the tobacco-growing areas of Fujian.【Method】The experiment included a control of natural tillage depth of 15 cm + mid-tillage soil cultivation(CK), tillage depth of 20 cm + mid-tillage soil cultivation(D1), tillage depth of 25 cm + mid-tillage soil cultivation(D2) and tillage depth of 25 cm + no mid-tillage soil cultivation(D3) in the tobacco-growing areas of Fujian. The study compared and analyzed the differences in yield and production value of flue-cured tobacco and the physicochemical properties of the soil under different treatments. Additionally, the high-throughput sequencing technology Illumina MiSeq was used to systematically analyze the differences in microbial structure and functional diversity in the rhizosphere under the deep tillage treatments. Spearman correlation coefficient and the random forest model were utilized to evaluate the correlation between the rhizosphere microbial community, soil nutrients and flue-cured tobacco yield.【Result】Deep tillage could significantly increase the yield and production value of flue-cured tobacco(P<0.05, the same below). Among the treatments, the D2 treatment had the best effect in terms of yield and efficiency improvement, but the improvement between the D2 and D3 treatments was not significantly different(P>0.05, the same below). In terms of soil properties, all deep tillage treatments could significantly improve soil total porosity and capillary porosity compared with CK. The content of alkali-hydrolyzed nitrogen, urease, sucrase and catalase activities increased with the deepening of tillage depth. Appropriate deep tillage treatment could significantly increase the bacterial α diversity. The relative abundance of Chloroflexi and Burkholderia increased significantly under deep tillage, while the relative abundance of Rhodanobacter decreased significantly. The results of Bugbase phenotypic prediction showed that deep tillage treatment could significantly increase the abundance of aerobic bacteria and gram-negative bacteria in rhizosphere soil. D2 and D3 treatments could significantly increase the relative abundance of oxidative stress tolerant bacteria compared with D1 treatment. The results of FAPROTAX function prediction showed that each deep tillage treatment could significantly improve the relative abundance of nutrient cycling functions such as nitrogen fixation and cellulolysis compared with CK. The random forest model predicted that nitrogen fixation was the main factor affecting the yield formation of flue-cured tobacco.【Conclusion】Under the current trend of shallow cultivation layer in the tobaccogrowing areas of Fujian, moderate deep tillage(25 cm) has a positive effect on improving the rhizosphere micro-ecological environment of flue-cured tobacco. However, the mid-tillage soil cultivation before the vigorous growth stage of fluecured tobacco under moderate deep tillage has no significant impact on the yield and production value of flue-cured tobacco.